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<title>Order parameters for individual leaflets — gorder "1.2.0" documentation</title>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Order parameters for individual leaflets</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#gorder.leaflets.ClusteringClassification"><code class="docutils literal notranslate"><span class="pre">ClusteringClassification</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="#gorder.leaflets.GlobalClassification"><code class="docutils literal notranslate"><span class="pre">GlobalClassification</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#gorder.leaflets.NdxClassification"><code class="docutils literal notranslate"><span class="pre">NdxClassification</span></code></a></li>
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<section id="module-gorder.leaflets">
<span id="order-parameters-for-individual-leaflets"></span><h1>Order parameters for individual leaflets<a class="headerlink" href="#module-gorder.leaflets" title="Link to this heading"></a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.leaflets.ClusteringClassification">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.leaflets.</span></span><span class="sig-name descname"><span class="pre">ClusteringClassification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">heads</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frequency</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flip</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.leaflets.ClusteringClassification" title="Link to this definition"></a></dt>
<dd><p>Assign lipids into leaflets using spectral clustering.</p>
<p>Reliable but very slow. Recommended for curved membranes, tubes and vesicles.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>heads</strong> (<em>str</em>) – Selection query specifying reference atoms representing lipid headgroups
(typically phosphorus atoms or phosphate beads).
There must be exactly one such atom/bead per lipid molecule.</p></li>
<li><p><strong>frequency</strong> (<em>Optional</em><em>[</em><em>Frequency</em><em>]</em>) – Frequency of classification. Defaults to every frame.</p></li>
<li><p><strong>collect</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><em>bool</em><em>, </em><em>str</em><em>]</em><em>]</em><em>, </em><em>default=False</em>) – Determines whether leaflet classification data are saved and exported.
By default (<cite>False</cite>), data are not saved.
If <cite>True</cite>, data are saved internally and accessible via the Python API, but not written to a file.
If a string is provided, data are saved and written to the specified output file.</p></li>
<li><p><strong>flip</strong> (<em>bool</em><em>, </em><em>default=False</em>) – Flip the assignment. Upper leaflet becomes lower leaflet and vice versa. The default value is False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.leaflets.GlobalClassification">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.leaflets.</span></span><span class="sig-name descname"><span class="pre">GlobalClassification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">membrane</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">heads</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frequency</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">membrane_normal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flip</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.leaflets.GlobalClassification" title="Link to this definition"></a></dt>
<dd><p>Assign lipids into leaflets based on the global membrane center of geometry.</p>
<p>Reliable for planar membranes and fast. Recommended for most membranes.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>membrane</strong> (<em>str</em>) – Selection query specifying all lipids forming the membrane.</p></li>
<li><p><strong>heads</strong> (<em>str</em>) – Selection query specifying reference atoms representing lipid headgroups
(typically phosphorus atoms or phosphate beads).
There must be exactly one such atom/bead per lipid molecule.</p></li>
<li><p><strong>frequency</strong> (<em>Optional</em><em>[</em><em>Frequency</em><em>]</em>) – Frequency of classification. Defaults to every frame.</p></li>
<li><p><strong>membrane_normal</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em>) – Membrane normal used for leaflet classification. Defaults to the membrane normal
specified for the entire Analysis.</p></li>
<li><p><strong>collect</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><em>bool</em><em>, </em><em>str</em><em>]</em><em>]</em><em>, </em><em>default=False</em>) – Determines whether leaflet classification data are saved and exported.
By default (<cite>False</cite>), data are not saved.
If <cite>True</cite>, data are saved internally and accessible via the Python API, but not written to a file.
If a string is provided, data are saved and written to the specified output file.</p></li>
<li><p><strong>flip</strong> (<em>bool</em><em>, </em><em>default=False</em>) – Flip the assignment. Upper leaflet becomes lower leaflet and vice versa. The default value is False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.leaflets.IndividualClassification">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.leaflets.</span></span><span class="sig-name descname"><span class="pre">IndividualClassification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">heads</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">methyls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frequency</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">membrane_normal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flip</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.leaflets.IndividualClassification" title="Link to this definition"></a></dt>
<dd><p>Assign lipids into leaflets based on the orientation of acyl chains.</p>
<p>Less reliable but very fast. Recommended for very large, undulating planar membranes.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>heads</strong> (<em>str</em>) – Selection query specifying reference atoms representing lipid headgroups
(typically phosphorus atoms or phosphate beads).
There must be exactly one such atom/bead per lipid molecule.</p></li>
<li><p><strong>methyls</strong> (<em>str</em>) – Selection query specifying reference atoms representing methyl groups at the ends of lipid tails.
There should be exactly one such atom/bead per acyl chain (e.g., two for lipids with two acyl chains).</p></li>
<li><p><strong>frequency</strong> (<em>Optional</em><em>[</em><em>Frequency</em><em>]</em>) – Frequency of classification. Defaults to every frame.</p></li>
<li><p><strong>membrane_normal</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em>) – Membrane normal used for leaflet classification. Defaults to the membrane normal
specified for the entire Analysis.</p></li>
<li><p><strong>collect</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><em>bool</em><em>, </em><em>str</em><em>]</em><em>]</em><em>, </em><em>default=False</em>) – Determines whether leaflet classification data are saved and exported.
By default (<cite>False</cite>), data are not saved.
If <cite>True</cite>, data are saved internally and accessible via the Python API, but not written to a file.
If a string is provided, data are saved and written to the specified output file.</p></li>
<li><p><strong>flip</strong> (<em>bool</em><em>, </em><em>default=False</em>) – Flip the assignment. Upper leaflet becomes lower leaflet and vice versa. The default value is False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.leaflets.LocalClassification">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.leaflets.</span></span><span class="sig-name descname"><span class="pre">LocalClassification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">membrane</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">heads</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">radius</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frequency</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">membrane_normal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flip</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.leaflets.LocalClassification" title="Link to this definition"></a></dt>
<dd><p>Assign lipids into leaflets based on the local membrane center of geometry.</p>
<p>Reliable for planar membranes but slow.
Recommended for planar membranes if the global and individual methods do not work for you.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>membrane</strong> (<em>str</em>) – Selection query specifying all lipids forming the membrane.</p></li>
<li><p><strong>heads</strong> (<em>str</em>) – Selection query specifying reference atoms representing lipid headgroups
(typically phosphorus atoms or phosphate beads).
There must be exactly one such atom/bead per lipid molecule.</p></li>
<li><p><strong>radius</strong> (<em>float</em>) – Radius of a cylinder used to calculate the local membrane center of geometry (in nm).</p></li>
<li><p><strong>frequency</strong> (<em>Optional</em><em>[</em><em>Frequency</em><em>]</em>) – Frequency of classification. Defaults to every frame.</p></li>
<li><p><strong>membrane_normal</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em>) – Membrane normal used for leaflet classification. Defaults to the membrane normal
specified for the entire Analysis.</p></li>
<li><p><strong>collect</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><em>bool</em><em>, </em><em>str</em><em>]</em><em>]</em><em>, </em><em>default=False</em>) – Determines whether leaflet classification data are saved and exported.
By default (<cite>False</cite>), data are not saved.
If <cite>True</cite>, data are saved internally and accessible via the Python API, but not written to a file.
If a string is provided, data are saved and written to the specified output file.</p></li>
<li><p><strong>flip</strong> (<em>bool</em><em>, </em><em>default=False</em>) – Flip the assignment. Upper leaflet becomes lower leaflet and vice versa. The default value is False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.leaflets.ManualClassification">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.leaflets.</span></span><span class="sig-name descname"><span class="pre">ManualClassification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frequency</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flip</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.leaflets.ManualClassification" title="Link to this definition"></a></dt>
<dd><p>Get leaflet assignment from an external YAML file or a dictionary.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>input</strong> (<em>Union</em><em>[</em><em>str</em><em>, </em><em>Mapping</em><em>[</em><em>str</em><em>, </em><em>ndarray</em><em>[</em><em>uint8</em><em>]</em><em>]</em><em>]</em>) – Path to the input YAML file containing the leaflet assignment
or a dictionary specifying the leaflet assignment.</p></li>
<li><p><strong>frequency</strong> (<em>Optional</em><em>[</em><em>Frequency</em><em>]</em>) – Frequency of classification. Defaults to every frame.</p></li>
<li><p><strong>flip</strong> (<em>bool</em><em>, </em><em>default=False</em>) – Flip the assignment. Upper leaflet becomes lower leaflet and vice versa. The default value is False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.leaflets.NdxClassification">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.leaflets.</span></span><span class="sig-name descname"><span class="pre">NdxClassification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ndx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">heads</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">upper_leaflet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lower_leaflet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frequency</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flip</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.leaflets.NdxClassification" title="Link to this definition"></a></dt>
<dd><p>Get leaflet assignment from NDX file(s).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ndx</strong> (<em>Sequence</em><em>[</em><em>str</em><em>]</em>) – A list of NDX files to read.</p></li>
<li><p><strong>heads</strong> (<em>str</em>) – Selection query specifying reference atoms representing lipid headgroups
(typically phosphorus atoms or phosphate beads).
There must be exactly one such atom/bead per lipid molecule.</p></li>
<li><p><strong>upper_leaflet</strong> (<em>str</em>) – Name of the group in the NDX file(s) specifying the atoms of the upper leaflet.</p></li>
<li><p><strong>lower_leaflet</strong> (<em>str</em>) – Name of the group in the NDX file(s) specifying the atoms of the lower leaflet.</p></li>
<li><p><strong>frequency</strong> (<em>Optional</em><em>[</em><em>Frequency</em><em>]</em>) – Frequency of classification. Defaults to every frame.</p></li>
<li><p><strong>flip</strong> (<em>bool</em><em>, </em><em>default=False</em>) – Flip the assignment. Upper leaflet becomes lower leaflet and vice versa. The default value is False.</p></li>
</ul>
</dd>
</dl>
<p class="rubric">Notes</p>
<ul class="simple">
<li><p>No glob expansion is performed for the NDX files.</p></li>
</ul>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="gorder.leaflets.SphericalClusteringClassification">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">gorder.leaflets.</span></span><span class="sig-name descname"><span class="pre">SphericalClusteringClassification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">heads</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">frequency</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flip</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#gorder.leaflets.SphericalClusteringClassification" title="Link to this definition"></a></dt>
<dd><p>Assign lipids into leaflets using gaussian mixture model.</p>
<p>Reliable for spherical vesicles and fast. Do not use for anything other than vesicles!</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>heads</strong> (<em>str</em>) – Selection query specifying reference atoms representing lipid headgroups
(typically phosphorus atoms or phosphate beads).
There must be exactly one such atom/bead per lipid molecule.</p></li>
<li><p><strong>frequency</strong> (<em>Optional</em><em>[</em><em>Frequency</em><em>]</em>) – Frequency of classification. Defaults to every frame.</p></li>
<li><p><strong>collect</strong> (<em>Optional</em><em>[</em><em>Union</em><em>[</em><em>bool</em><em>, </em><em>str</em><em>]</em><em>]</em><em>, </em><em>default=False</em>) – Determines whether leaflet classification data are saved and exported.
By default (<cite>False</cite>), data are not saved.
If <cite>True</cite>, data are saved internally and accessible via the Python API, but not written to a file.
If a string is provided, data are saved and written to the specified output file.</p></li>
<li><p><strong>flip</strong> (<em>bool</em><em>, </em><em>default=False</em>) – Flip the assignment. Upper leaflet becomes lower leaflet and vice versa. The default value is False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
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